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Sample GSM1139139 Query DataSets for GSM1139139
Status Public on May 13, 2013
Title Cdk9_ChIPSeq
Sample type SRA
 
Source name Murine erythroleukemia (MEL) cells
Organism Mus musculus
Characteristics cell line: non-induced C88 MEL cells
chip antibody: CDK9 C20 antibody (Santa Cruz Biotechnology, C20, sc-484)
Growth protocol MEL cell lines were maintained in DMEM supplemented with 10% fetal calf serum and penicillin/streptomycin.
Extracted molecule genomic DNA
Extraction protocol 10 ng of ChIPped DNA was end-repaired, ligated to adapters, size selected on gel (200±25 bp range) and PCR amplified using Phusion polymerase. Cluster generation was performed using the Illumina Cluster Reagents preparation.
ChIP-Seq library was prepared according to the Illumina protocol (www.illumina.com).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing 36 bp raw reads were mapped against mm9/NCBI build 37.1 of the mouse genome with ELAND (Illumina).
Uniquely mapped reads were extended to 200 bp and then transformed into the genome-wide reads density (coverage) with the ShortRead Bioconductor package.
The coverage from ChIP and IgG control was then normalized to have equal levels of background signal.
The method used to normalize was modified from Peakseq (Rozowsky et al. 2009).
After normalization, tracks of coverage profiles for all factors and IgG control were uploaded and visualized by the UCSC genome browser.
The coverage from all factors was subtracted from the normalized coverage from the corresponding IgG controls.
Genome_build: MGSCv37
Supplementary_files_format_and_content: BigWig files
 
Submission date May 12, 2013
Last update date May 15, 2019
Contact name Supat Thongjuea
E-mail(s) supat.thongjuea@ndcls.ox.ac.uk
Organization name The Weatherall Institute of Molecular Medicine
Department MRC Molecular Haematology Unit
Street address Headington
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platform ID GPL13112
Series (1)
GSE46849 In vivo live imaging of RNA polymerase II transcription factories in primary cells
Relations
BioSample SAMN02142118
SRA SRX277329
Named Annotation GSM1139139_Cdk9_C20.normalized.BigWig

Supplementary file Size Download File type/resource
GSM1139139_Cdk9_C20.normalized.BigWig 300.9 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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